Hi,
first of all thank you for your comprehensive feedback.
This plugin is primarily a loot plugin and the furnace configuration is just intended to be a small addition. I recommend you to use a more specialized plugin to control furnaces if this one doesn't fit your needs.
You are also not the first one to request more categories and sub-categories. The problem is that with the current percentage-based system, the plugin would have to do significantly more computation for each loot spawn if there were more categories or even sub-categories. The only way to avoid this would be switching to a weight-based system which is what AlphaLoot and also rust itself use by default. However this system would be far less intuitive to configure (in my opinion). In the end its a decision between performance and ease of use.
For your last suggestion, I'm gonna add a button in the future that allows you to add new items to all crates that they spawn in by default (with the default amount and the default chance). Just keep in mind that you will still have to adjust chances and amounts later on to fit your configuration, this can not be done automatically.